[2024-01-24 13:57:13,589] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:13,591] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:13,591] [INFO] DQC Reference Directory: /var/lib/cwl/stge34f1b14-cd73-46b4-a52a-e5dcbd69f7a9/dqc_reference
[2024-01-24 13:57:14,894] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:14,895] [INFO] Task started: Prodigal
[2024-01-24 13:57:14,895] [INFO] Running command: gunzip -c /var/lib/cwl/stgb5862ca0-46c4-4233-a93b-3719bf0c2bef/GCF_900111355.1_IMG-taxon_2634166323_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900111355.1_IMG-taxon_2634166323_annotated_assembly_genomic.fna/cds.fna -a GCF_900111355.1_IMG-taxon_2634166323_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:20,292] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:20,292] [INFO] Task started: HMMsearch
[2024-01-24 13:57:20,292] [INFO] Running command: hmmsearch --tblout GCF_900111355.1_IMG-taxon_2634166323_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge34f1b14-cd73-46b4-a52a-e5dcbd69f7a9/dqc_reference/reference_markers.hmm GCF_900111355.1_IMG-taxon_2634166323_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:20,542] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:20,544] [INFO] Found 6/6 markers.
[2024-01-24 13:57:20,572] [INFO] Query marker FASTA was written to GCF_900111355.1_IMG-taxon_2634166323_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:57:20,573] [INFO] Task started: Blastn
[2024-01-24 13:57:20,573] [INFO] Running command: blastn -query GCF_900111355.1_IMG-taxon_2634166323_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stge34f1b14-cd73-46b4-a52a-e5dcbd69f7a9/dqc_reference/reference_markers.fasta -out GCF_900111355.1_IMG-taxon_2634166323_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:21,198] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:21,201] [INFO] Selected 24 target genomes.
[2024-01-24 13:57:21,202] [INFO] Target genome list was writen to GCF_900111355.1_IMG-taxon_2634166323_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:57:21,209] [INFO] Task started: fastANI
[2024-01-24 13:57:21,209] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5862ca0-46c4-4233-a93b-3719bf0c2bef/GCF_900111355.1_IMG-taxon_2634166323_annotated_assembly_genomic.fna.gz --refList GCF_900111355.1_IMG-taxon_2634166323_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900111355.1_IMG-taxon_2634166323_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:30,434] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:30,435] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge34f1b14-cd73-46b4-a52a-e5dcbd69f7a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:30,436] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge34f1b14-cd73-46b4-a52a-e5dcbd69f7a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:30,451] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:30,451] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:30,452] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Isobaculum melis	strain=DSM 13760	GCA_900111355.1	142588	142588	type	True	100.0	913	916	95	conclusive
Carnobacterium divergens	strain=NCTC13772	GCA_900446755.1	2748	2748	type	True	78.2194	141	916	95	below_threshold
Carnobacterium divergens	strain=DSM 20623	GCA_001437085.1	2748	2748	type	True	78.18	137	916	95	below_threshold
Carnobacterium divergens	strain=66	GCA_000744255.1	2748	2748	type	True	78.1595	135	916	95	below_threshold
Carnobacterium viridans	strain=MPL-11	GCA_900102725.1	174587	174587	type	True	77.5681	72	916	95	below_threshold
Carnobacterium jeotgali	strain=MS3	GCA_000745125.1	545534	545534	type	True	77.4577	77	916	95	below_threshold
Carnobacterium mobile	strain=MT37L	GCA_000744825.1	2750	2750	type	True	77.225	71	916	95	below_threshold
Vagococcus bubulae	strain=SS1994	GCA_003950315.1	1977868	1977868	type	True	77.056	79	916	95	below_threshold
Enterococcus saccharolyticus subsp. saccharolyticus	strain=ATCC 43076	GCA_000407005.1	1814218	41997	type	True	76.8188	83	916	95	below_threshold
Enterococcus pseudoavium	strain=NBRC 100491	GCA_001544295.1	44007	44007	type	True	76.8177	59	916	95	below_threshold
Enterococcus hermanniensis	strain=DSM 17122	GCA_001885945.1	249189	249189	type	True	76.757	59	916	95	below_threshold
Enterococcus saccharolyticus subsp. saccharolyticus	strain=ATCC 43076	GCA_000407285.1	1814218	41997	type	True	76.737	79	916	95	below_threshold
Enterococcus saccharolyticus	strain=DSM 20726	GCA_001886235.1	41997	41997	type	True	76.6563	75	916	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:30,453] [INFO] DFAST Taxonomy check result was written to GCF_900111355.1_IMG-taxon_2634166323_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:57:30,454] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:30,454] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:30,454] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge34f1b14-cd73-46b4-a52a-e5dcbd69f7a9/dqc_reference/checkm_data
[2024-01-24 13:57:30,456] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:30,490] [INFO] Task started: CheckM
[2024-01-24 13:57:30,491] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900111355.1_IMG-taxon_2634166323_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900111355.1_IMG-taxon_2634166323_annotated_assembly_genomic.fna/checkm_input GCF_900111355.1_IMG-taxon_2634166323_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:57:54,825] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:54,826] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:54,848] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:54,848] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:54,848] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900111355.1_IMG-taxon_2634166323_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:57:54,849] [INFO] Task started: Blastn
[2024-01-24 13:57:54,849] [INFO] Running command: blastn -query GCF_900111355.1_IMG-taxon_2634166323_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stge34f1b14-cd73-46b4-a52a-e5dcbd69f7a9/dqc_reference/reference_markers_gtdb.fasta -out GCF_900111355.1_IMG-taxon_2634166323_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:55,724] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:55,727] [INFO] Selected 25 target genomes.
[2024-01-24 13:57:55,728] [INFO] Target genome list was writen to GCF_900111355.1_IMG-taxon_2634166323_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:55,739] [INFO] Task started: fastANI
[2024-01-24 13:57:55,740] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5862ca0-46c4-4233-a93b-3719bf0c2bef/GCF_900111355.1_IMG-taxon_2634166323_annotated_assembly_genomic.fna.gz --refList GCF_900111355.1_IMG-taxon_2634166323_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900111355.1_IMG-taxon_2634166323_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:09,170] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:09,189] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:09,189] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_900111355.1	s__Isobaculum melis	100.0	913	916	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Isobaculum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000744255.1	s__Carnobacterium divergens	78.1687	134	916	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium	95.0	99.06	98.93	0.92	0.90	24	-
GCF_900258435.1	s__Carnobacterium divergens_A	78.0146	149	916	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium	95.0	99.21	98.87	0.95	0.92	17	-
GCF_900102725.1	s__Carnobacterium_A viridans	77.5681	72	916	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A	95.0	98.44	98.44	0.88	0.88	2	-
GCF_000745125.1	s__Carnobacterium_A jeotgali	77.4577	77	916	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A	95.0	99.33	98.67	0.94	0.87	3	-
GCF_000746825.1	s__Carnobacterium_A inhibens	77.4179	78	916	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A	95.0	98.16	98.07	0.90	0.88	3	-
GCF_000744285.1	s__Carnobacterium_A pleistocenium	77.3913	75	916	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001730295.1	s__Enterococcus plantarum	77.3041	102	916	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	98.57	98.46	0.89	0.88	4	-
GCF_000744825.1	s__Carnobacterium_A mobile	77.2652	70	916	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A	95.0	97.99	97.99	0.87	0.87	2	-
GCF_900115825.1	s__Desemzia incerta	77.2624	50	916	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Desemzia	95.0	97.61	97.61	0.88	0.88	2	-
GCF_014397115.1	s__Vagococcus carniphilus	77.2105	96	916	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900163795.1	s__Vagococcus fluvialis_A	77.1709	82	916	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_017316185.1	s__Vagococcus sp017316185	77.1391	87	916	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000195575.1	s__Carnobacterium_A sp000195575	77.1081	70	916	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003950315.1	s__Vagococcus bubulae	77.056	79	916	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017316125.1	s__Enterococcus_B sp017316125	76.9757	77	916	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013874835.1	s__WM01 sp013874835	76.9399	55	916	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__WM01	95.0	99.19	98.77	0.92	0.86	4	-
GCF_000407285.1	s__Enterococcus_F saccharolyticus	76.737	79	916	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_F	95.0	99.99	99.99	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:09,191] [INFO] GTDB search result was written to GCF_900111355.1_IMG-taxon_2634166323_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:09,192] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:09,196] [INFO] DFAST_QC result json was written to GCF_900111355.1_IMG-taxon_2634166323_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:58:09,196] [INFO] DFAST_QC completed!
[2024-01-24 13:58:09,196] [INFO] Total running time: 0h0m56s